---
title: "CE4 - Dashboard COVID-19"
output: 
  flexdashboard::flex_dashboard:
    orientation: columns
    vertical_layout: fill
    source_code: embed
    social: menu
    theme: cosmo
    self_contained: FALSE 
    fig_mobile: TRUE
---



```{r libraries, message=F, warning=F}
library(flexdashboard)
library(rio)
library(tidyverse)
library(XML)
library(httr)
library(RCurl)
library(sf)
library(lubridate)
library(leaflet)
library(colorspace)
library(DT)
library(zoo)
library(slider)
library(plotly)
library(waffle)
library(extrafont)
library(plyr)
library(extrafont)
library(waffle)
library(RColorBrewer)
options(scipen=999)
```

```{r imports, message=F, warning=F, include = F, echo =F}
nac <- rio::import("https://github.com/jincio/COVID_19_PERU/blob/master/reportes_minsa.xlsx?raw=true")

deps <- rio::import("https://github.com/jincio/COVID_19_PERU/blob/master/reportes_minsa.xlsx?raw=true", sheet = 2)

pop <- read_csv("data/peru_pop_stratum.csv") %>%
  group_by(dep_adm1) %>%
  dplyr::summarise(pop = sum(N)) %>%
  dplyr::mutate(REGION = toupper(dep_adm1))


Paises_LATAM <- c("Argentina","Bolivia","Brazil","Chile","Colombia","Ecuador","Mexico","Peru","Uruguay","Venezuela")
LATAM <- read_csv ("https://covid.ourworldindata.org/data/owid-covid-data.csv") %>%
  dplyr::filter(location %in% Paises_LATAM) %>%
  dplyr::mutate( mav_new = slide_dbl(new_cases, ~mean(.x, na.rm = TRUE), .before = 6))

shp <- st_read("Limite_departamental", stringsAsFactors = F)%>% 
  st_transform(4326) %>% 
  dplyr::select(Departamento = NOMBDEP)
```

```{r global, message=F, warning=F}
c.date <- max(deps$Fecha)
y.date <- as.Date(c.date) - 1 
date <- ymd(Sys.Date())
f.date <- min(deps$Fecha)
```

```{r plotly, message=F, warning=F}

plotly_config <- function(x) {
  x %>% config(locale = "es",
               displaylogo=F,
               modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                          "drawclosedpath","drawopenpath",
                                          "hoverClosestCartesian","hoverCompareCartesian",
                                          "toggleHover","toggleSpikelines"),
               responsive = T
  )
}




# %>%
#   add_segments(x = "2020-03-15", xend = "2020-03-15", 
#                y = 0, yend=roundUpNice(max(nac$pos.new)),
#                text="2020-04-08",name="Estado de Emergencia",
#                hovertemplate = paste('%{text}'),
#                legendgroup = 'group2',
#                width=2, 
#                line = list(color = "#7aa82a", 
#                            width = 3, 
#                            dash = "dot")
#   ) %>%
#   add_segments(x = "2020-03-26", xend = "2020-03-26", 
#                y = 0, yend=roundUpNice(max(nac$pos.new)),
#                text="2020-04-08",name="1ra ampliación",
#                hovertemplate = paste('%{text}'),
#                legendgroup = 'group2',
#                width=2, 
#                line = list(color = "#7aa82a", 
#                            width = 3, 
#                            dash = "dot")
#                ) %>%
#   add_segments(x = "2020-04-23", xend = "2020-04-23", 
#                y = 0, yend=roundUpNice(max(nac$pos.new)),
#                text="2020-04-08",name="3ra ampliación",
#                hovertemplate = paste('%{text}'),
#                legendgroup = 'group2',
#                width=2, 
#                line = list(color = "#7aa82a", 
#                            width = 3, 
#                            dash = "dot")
#                ) 

```

```{r maps, message=F, warning=F}
map_tiles <- function(x) {
  x %>% 
    addTiles(urlTemplate = 'http://a.basemaps.cartocdn.com/dark_all/{z}/{x}/{y}.png',
             options = providerTileOptions(minZoom = 5, maxZoom = 6))
}

map_bounds <- function(x) {
  x %>% setMaxBounds(lng1 = -90.648918,
                     lat1 = 4.991423,
                     lng2 = -59.605965,
                     lat2 = -23.920121) 
}

map_poly <-  function(x,y,z) {
  x %>%
    addPolygons(fillColor = pal.cases(log(y)),
                weight = 2,
                opacity = 1,
                color = "white",
                dashArray = "",
                fillOpacity = 0.7,
                highlight = highlightOptions(
                  weight = 5,
                  color = "#666",
                  dashArray = "",
                  fillOpacity = 0.7,
                  bringToFront = TRUE),
                label = z,
                labelOptions = labelOptions(
                  style = list("font-weight" = "normal", padding = "3px 8px"),
                  textsize = "15px",
                  direction = "auto")) 
  
}

```

```{r deps, message=F, warning=F}
## Procesamiento de los datos por región.

dep <- 
  deps %>% 
  dplyr::select(dat = Fecha,
                dep = REGION, 
                pos = Positivos_totales, 
                pos.imp = PositivosImputados_totales,
                pas =Fallecidos, 
                smp =Total_muestras
  ) %>% 
  dplyr::mutate(pas = pas %>% if_else(is.na(.), 0, .),
                dat = as.Date(dat)
  ) %>% 
  group_by(dep
  ) %>% 
  dplyr::mutate(pos.new = pos - lag(pos, n = 1),
                pos.imp.new = pos.imp - lag(pos.imp, n = 1),
                pas.new = lag(pas, n = 1),
                smp.new = lag(smp, n = 1),
                ratio.new = signif(pos.new/smp.new), digits = 3,
                days.start =as.numeric(dat-first(dat), unit="days"),
                dummy = days.start+20,
                dup.1 = exp((log(2)/1)*days.start),
                dup.2 = exp((log(2)/2)*days.start),
                dup.3 = exp((log(2)/3)*days.start),
                dup.4 = exp((log(2)/4)*days.start),
                days.end = difftime(date, dat , units = c("days")),
                mav.pos.new = slide_dbl(pos.new, ~mean(.x, na.rm = TRUE), .before = 6),
                ) %>%
  merge(pop %>% 
          select(dep = REGION, pop)
        ) %>% 
  dplyr::mutate(pos.hab = pos/pop*100000,
         smp.hab = smp/pop*100000,
         pos.new.hab = smp/pop*100000,
         mav.pos.new.hab = mav.pos.new/pop*1000000)

## Poligonos y data regional - Mapas

geom.dep <- dep %>% 
  merge(shp, by.y = 'Departamento', by.x = 'dep', all.x = T) %>%
  st_as_sf(sf_column_name = 'geometry') 

rm(shp) # No more use for shp

## Datos a nivel Nacional

nac <- dep %>%
  select(-c("dep")) %>%
  group_by(dat) %>%
  dplyr::mutate_at(vars(-c("dat","dup.1","dup.2","dup.3","dup.4")),sum, na.rm = T) %>%
  dplyr::summarize_all(list(max)) %>%
  dplyr::mutate(days.end = difftime(date, dat , units = c("days")),
                days.start = as.numeric(difftime(dat,f.date), units="days"))

dup.nac <- data.frame(dat = as.Date(seq(1,30, 1)+date)) %>%
  dplyr::mutate(days.start = as.numeric(difftime(dat,f.date), units="days"),
                dummy = days.start+20,
                dup.1 = exp((log(2)/1)*days.start),
                dup.2 = exp((log(2)/2)*days.start),
                dup.3 = exp((log(2)/3)*days.start),
                dup.4 = exp((log(2)/4)*days.start)
  ) %>%
  bind_rows(nac)

## Datos del día de hoy
c.dep <- geom.dep %>%
  dplyr::filter(dat == c.date)

## Formato Regiones Wide
dep.pos <-  dep %>%
  select(dat,dep,pos,days.end) %>%
  spread(dep, pos) %>% 
  dplyr::rename(LA_LIBERTAD = `LA LIBERTAD`,
                MADRE_DE_DIOS = `MADRE DE DIOS`,
                SAN_MARTIN = `SAN MARTIN`) 


dep.mav.pos.new<-  dep %>%
  dplyr::select(dat,dep,days.end,mav.pos.new) %>%
  spread(dep, mav.pos.new) %>% 
  dplyr::rename(LA_LIBERTAD = `LA LIBERTAD`,
                MADRE_DE_DIOS = `MADRE DE DIOS`,
                SAN_MARTIN = `SAN MARTIN`) 


dep.pos.imp.new <- dep %>%
  select(dat,dep,days.end,pos.imp.new) %>%
  spread(dep, pos.imp.new) %>% 
  dplyr::rename(LA_LIBERTAD = `LA LIBERTAD`,
                MADRE_DE_DIOS = `MADRE DE DIOS`,
                SAN_MARTIN = `SAN MARTIN`) 


```

```{r, message=F, warning=F}

vars.pmav.new <- dep %>%
  dplyr::select(dat,dep,mav.pos.new.hab) %>% 
  dplyr::filter(dat == c.date) %>% 
  dplyr::arrange(dplyr::desc(mav.pos.new.hab)) %>%
  dplyr::select(dep) %>%
  dplyr::mutate(dep = ifelse(dep=="LA LIBERTAD","LA_LIBERTAD",
                                ifelse(dep=="MADRE DE DIOS","MADRE_DE_DIOS",
                                       ifelse(dep=="SAN MARTIN","SAN_MARTIN",dep))))%>% 
  .$dep

vars.mav.new <- dep %>%
  dplyr::select(dat,dep,mav.pos.new) %>% 
  dplyr::filter(dat == c.date) %>% 
  dplyr::arrange(dplyr::desc(mav.pos.new)) %>%
  dplyr::select(dep) %>%
  dplyr::mutate(dep = ifelse(dep=="LA LIBERTAD","LA_LIBERTAD",
                                ifelse(dep=="MADRE DE DIOS","MADRE_DE_DIOS",
                                       ifelse(dep=="SAN MARTIN","SAN_MARTIN",dep))))%>% 
  .$dep
last.mav.new <- vars.mav.new[length(vars.mav.new)]


vars.pos <- dep %>%
  dplyr::select(dat,dep,pos) %>% 
  dplyr::filter(dat == c.date) %>% 
  dplyr::arrange(dplyr::desc(pos)) %>%
  dplyr::select(dep) %>%
  dplyr::mutate(dep = ifelse(dep=="LA LIBERTAD","LA_LIBERTAD",
                                ifelse(dep=="MADRE DE DIOS","MADRE_DE_DIOS",
                                       ifelse(dep=="SAN MARTIN","SAN_MARTIN",dep))))%>% 
  .$dep
last.pos <- vars.pos[length(vars.pos)]

```

Casos Acumulados {.bg}
=====================================  

Mapas {.tabset data-width=250} 
-------------------------------------

### Casos

```{r, message=F, warning=F}
palette_1 <- c("#ffffff",
               "#fff3e3",
               "#ffe8c8",
               "#ffddac",
               "#ffd291",
               "#ffc775",
               "#ffbc59",
               "#ffb139", #ffa600
               "#ec9832",
               "#d8802c",
               "#c26926",
               "#ac5320",
               "#953e1b",
               "#7d2914",
               "#65150d",
               "#4e0000")

labels.total <-  sprintf(
  "%s
Casos: %s",
  c.dep$dep, c.dep$pos) %>% lapply(htmltools::HTML)

pal.cases <- colorNumeric( palette=palette_1, domain = log(c.dep$pos), na.color="transparent")

leaflet(c.dep) %>%
  map_tiles() %>%
  map_poly (c.dep$pos,labels.total)  %>%
  addLegend("bottomleft", pal = pal.cases, values = log(c.dep$pos), title= 'Casos', labFormat = labelFormat(transform = function(x) round(exp(x)))) %>% 
  map_bounds ()
    
```

### Casos / 100k hab

```{r, message=F, warning=F}
labels.pos.hab <- sprintf(
  "%s
Casos/100k hab: %s",
  c.dep$dep, round(c.dep$pos.hab)) %>% lapply(htmltools::HTML)

pal.cases <- colorNumeric( palette=palette_1, domain = log(c.dep$pos.hab), na.color="transparent")

leaflet(c.dep) %>%
  map_tiles () %>%
  map_poly (c.dep$pos.hab,labels.pos.hab) %>%
  addLegend("bottomleft", pal = pal.cases, values = log(c.dep$pos.hab), title= 'Casos', labFormat = labelFormat(transform = function(x) round(exp(x)))) %>% map_bounds
```

Nacional {.tabset data-width=300} 
-------------------------------------

### Lineal
```{r function.roundup}
# https://stackoverflow.com/questions/6461209/how-to-round-up-to-the-nearest-10-or-100-or-x
# Rounds Up to a nice number, defined as a number divisible by those in the vector.
# Some other good choices of the "nice" vector above are: 1:10, c(1,5,10), seq(1, 10, 0.1),c(1,2,4,5,6,8,10)

roundUpNice <- function(x, nice=c(1,2,5,6,10)) {
    if(length(x) != 1) stop("'x' must be of length 1")
    10^floor(log10(x)) * nice[[which(x <= 10^floor(log10(x)) * nice)[[1]]]]
}
# roundUpNice(max(nac$pos.new))/5
```



```{r, message=F, warning=F}
nac %>%
  plot_ly()%>% 
  add_trace(x = ~dat, y = ~pos, 
            type = 'scatter',
            mode = 'lines+markers', 
            name = 'Casos Acumulados',
            line = list(color = '#ffa600'), 
            marker = list(color = '#ffa600'),
            text = paste(nac$days.end, "días desde hoy"),
            hovertemplate = ~paste('Fecha: %{x}',
                                   "
Casos Acumulados: %{y:.0f}
",
                                   '%{text}'),
            yaxis="y2") %>%
  add_trace(x = ~dat, y = ~pos.new, 
            type = 'bar', name = 'Casos Nuevos',
            marker = list(color = '#006b7d'), 
            text = paste(nac$days.end, "días desde hoy"),
            hovertemplate = paste('Fecha: %{x}',
                                  '
Nuevos Casos: %{y}
',
                                  '%{text}'))  %>%
  add_segments(x = "2020-04-08", xend = "2020-04-08", 
               y = 0, yend=roundUpNice(max(nac$pos.new)),
               text="2020-04-08",name="Pruebas Rápidas",
               hovertemplate = paste('%{text}'),
               legendgroup = 'group2',
               width=2, 
               line = list(color = "#008f6a", 
                           width = 3, 
                           dash = "dot"))%>% 
  layout(title = 'Casos nuevos y acumulados - Perú',
         titlefont=list(color="white"),
         xaxis = list(title = "Fecha de Reporte",
                      color = "white"),
         yaxis = list(side = 'left', title = 'Casos Nuevos por día', 
                      showgrid = T, gridcolor = "#818181", zeroline = F,
                      color = "#98cbe1",
                      range=list(0, roundUpNice(max(nac$pos.new))),
                      autotick=F,
                      tick0=0,
                      dtick=roundUpNice(max(nac$pos.new))/5),
         yaxis2 = list(side = 'right', overlaying = "y",
                       title = 'Casos acumulados (lineal)', 
                       showgrid = F, zeroline = F,
                       color = "#ffd29f",
                       range=list(0, roundUpNice(max(nac$pos))),
                      autotick=F,
                      tick0=0,
                      dtick=roundUpNice(max(nac$pos))/5),
         legend = list(orientation = "h",  
                       xanchor = "center",
                       yanchor = "bottom",
                       x = 0.5,
                       y = -0.125,
                       font = list(color = "white")),
         paper_bgcolor="black",
         plot_bgcolor="black",
         hovermode = "closest",
         hoverdistance = 50,
         dragmode="pan",
         margin = list(l=65, r=65, b=40, t=50),
         autosize=T
  ) %>% 
  plotly_config
  

```

### Logaritmico 

```{r, message=F, warning=F}
nac %>%
  plot_ly() %>%
  add_trace(x = ~dat, y = ~pos.new, 
            type = 'bar', name = 'Casos Nuevos',
            marker = list(color = '#006b7d'), 
            text = paste(nac$tm, "días desde hoy"),
            hovertemplate = paste('Fecha: %{x}',
                                  '
Nuevos Casos: %{y}
',
                                  '%{text}'))%>% 
  add_trace(x = ~dat, y = ~pos, 
            type = 'scatter',
            mode = 'lines+markers', 
            name = 'Casos Acumulados', 
            yaxis = 'y2',
            line = list(color = '#ffa600'), 
            marker = list(color = '#ffa600'),
            text = paste(nac$tm, "días desde hoy"),
            hovertemplate = ~paste('Fecha: %{x}',
                                   "
Casos Acumulados: %{y:.0f}
",
                                   '%{text}')) %>%
  add_segments(x = "2020-04-08", xend = "2020-04-08", 
               y = 0, yend=max(nac$pos.new),
               text="2020-04-08",name="Inicio de P.R's",
               hovertemplate = paste('%{text}'),
               legendgroup = 'group2',
               width=2, 
               line = list(color = "#7aa82a", 
                           width = 3, 
                           dash = "dot")
  ) %>% 
  layout(title = 'Casos nuevos y acumulados - Perú',
         titlefont=list(color="white"),
         xaxis = list(title = "Fecha de reporte",
                      color ="white"),
         yaxis = list(side = 'left', title = 'Casos Nuevos por día (lineal)', 
                      showgrid = FALSE, zeroline = FALSE,
                      color="white"),
         yaxis2 = list(side = 'right', overlaying = "y", type = "log",
                       title = 'Casos acumulados por día (logaritmica)', 
                       showgrid = FALSE, zeroline = FALSE,
                       tickmode = "linear",
                       tick0 = 0,
                       color="white"),
         legend = list(orientation = "h",  
                       xanchor = "center",
                       yanchor = "bottom",
                       x = 0.5,
                       y = -0.125,
                       font = list(color = "white")),
         paper_bgcolor="black",
         plot_bgcolor="black",
         hovermode = "closest",
         hoverdistance = 50,
         dragmode="pan",
         margin = list(l=65, r=65, b=40, t=50)
  ) %>% plotly_config
```

### Duplicación

```{r, message=F, warning=F}

plot_ly(dup.nac) %>%
  add_trace(x = ~days.start,  y = ~pos, 
            type = 'scatter',
            mode = 'lines+markers', 
            name = 'Casos Acumulados',
            line = list(color = '#ffa600'), 
            marker = list(color = '#ffa600'),
            hovertemplate = ~paste("
Casos Acumulados: %{y:.d0}
"),
            legendgroup = 'group1') %>% 
  add_trace(x = ~days.start, y = ~dup.1,
            mode = 'lines', 
            name = 'Casos se duplican en un (1) día',
            line = list(color = '#0e5871',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en un (1) día",
            hoverinfo = "text",
            legendgroup = 'group2') %>% 
  add_trace(x = ~days.start,y = ~dup.2,
            mode = 'lines', 
            name = 'Casos se duplican en dos (2) días',
            line = list(color = '#006b7d',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en dos (2) días",
            hoverinfo = "text",
            legendgroup = 'group2') %>% 
  add_trace(x = ~days.start,y = ~dup.3,
            mode = 'lines', 
            name = 'Casos se duplican en tres (3) días',
            line = list(color = '#007e7b',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en tres (3) días",
            hoverinfo = "text",
            legendgroup = 'group2') %>% 
  add_trace(x = ~days.start,y = ~dup.4,
            mode = 'lines', 
            name = 'Casos se duplican en cuatro (4) días',
            line = list(color = '#008f6a',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en tres (4) días",
            hoverinfo = "text",
            legendgroup = 'group2')  %>% 
  layout(title = 'Total de casos acumulados',
         titlefont=list(color="white"),
         xaxis = list(title = "Días desde el primer reporte",
                      range = c(as.Date(min(f.date)),max(date+15)),
                      color ="white"),
         yaxis = list(side = 'left', title = 'Total de casos acumulados', type="log", range = c(min(0),
                                 max(6)),
                      showgrid = FALSE, zeroline = FALSE,
                      tickmode = "linear",
                      color ="white"),
         legend = list(orientation = "h",  
                       xanchor = "center",
                       yanchor = "bottom",  
                       x = 0.5,
                       y = -0.25,
                       font = list(color = "white")),
         paper_bgcolor="black",
         plot_bgcolor="black",
         hovermode = "closest",
         hoverdistance = 50,
         dragmode="pan",
         margin = list(l=50, r=50, b=30, t=50)
  ) %>% plotly_config

```


Regional {.tabset data-width=350} 
-------------------------------------
```{r, message=F, warning=F}
y<- dep.pos.imp.new 
colnames(y) <- paste(colnames(y), "2", sep = "_")

y<- y %>% 
  select(-c("dat_2","days.end_2")) %>% 
  cbind(dep.pos)

```

### Acumulados - Lineal

```{r, message=F, warning=F}

plots <- lapply(vars.pos, function(var) {

  plot_ly(y) %>%
    add_lines(x = ~dat, 
              y = as.formula(paste0("~", var)),
              text = paste(dep.pos$days.end, "días desde hoy"),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Media Móvil: %{y:.2f}
',
                                    '%{text}'),
              name = ifelse(var == last.pos,"Media Móvil",var),
              legendgroup = 'group1',
              showlegend = ifelse(var == last.pos,TRUE,FALSE), 
              line = list(color = "#ffa600", 
                          width = 4)
    ) %>%
    add_segments(x = "2020-04-08", xend = "2020-04-08", 
                 y = 0, yend = max(dep.pos[var],na.rm = T),
                 text="2020-04-08", name="Inicio de P.R's",
                 hovertemplate = paste('%{text}'),
                 legendgroup = 'group2',
                 showlegend = ifelse(var == last.pos,TRUE,FALSE), 
                 line = list(color = "#7aa82a", 
                             width = 3, 
                             dash = "dot")
    )%>%
    add_trace(x = ~dat, y = as.formula(paste0("~", var,"_2")),
              type = 'bar', name = 'Casos Nuevos',
              marker = list(color = '#006b7d'), 
              text = paste(dep.pos.imp.new$days.end, "días desde hoy"),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Nuevos Casos: %{y}
',
                                    '%{text}'),
              showlegend = ifelse(var == last.pos,TRUE,FALSE)
              ) %>%
    layout(xaxis = list(range = c(min(dep.pos.imp.new$dat),
                                  max(dep.pos.imp.new$dat)),
                        color = "white"),
           yaxis = list(color = "white"),
           annotations = list(text = ifelse(var=="LA_LIBERTAD","LA LIBERTAD",
                                            ifelse(var=="MADRE_DE_DIOS","MADRE DE DIOS",
                                                   ifelse(var=="SAN_MARTIN","SAN MARTIN",paste0("",var,"")))),
                              x = 0,y = 1.15,
                              yref = "paper",xref = "paper",
                              xanchor = "left",yanchor = "top",
                              showarrow = FALSE,
                              font = list(size = 16,
                                          color = "white")),
           paper_bgcolor="black",
           plot_bgcolor="black",
           legend = list(orientation = "h",  
                         xanchor = "center",
                         yanchor = "bottom",
                         x = 0.5,
                         y = -0.125,
                         font = list(color = "white")),
           showlegend =T)
})

subplot(plots,nrows=5, shareX = T, titleX = F) %>%
  layout(title = list(text = "Total de casos confirmados - Acumulado Lineal",
                      font = list(size = 24,
                                  color="white")),
         annotations = list(
           list(text = "Fecha de reporte",
                x = 0.5,
                y = -0.09,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color = "white")),
           list(text = "Total de casos confirmados",
                x = -0.05,
                y = 0.5,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color ="white"),
                textangle = -90)),
         hovermode = "closest",
         hoverdistance = 10,
         dragmode="pan",
         margin = list(l=75, r=0, b=65, t=60)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines")
  )

```

### Acumulados - Logaritmico

```{r, message=F, warning=F}

plots <- lapply(vars.pos, function(var) {

  plot_ly(dep.pos) %>%
    add_lines(x = ~dat, 
              y = as.formula(paste0("~", var)),
              text = paste(dep.pos$days.end, "días desde hoy"),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Media Móvil: %{y:.2f}
',
                                    '%{text}'),
              name = ifelse(var == last.pos,"Media Móvil",var),
              legendgroup = 'group1',
              showlegend = ifelse(var == last.pos,TRUE,FALSE), 
              line = list(color = "#ffa600", 
                          width = 4)
    ) %>%
    add_segments(x = "2020-04-08", xend = "2020-04-08", 
                 y = 0, yend = max(dep.pos[var],na.rm = T),
                 text="2020-04-08", name="Inicio de P.R's",
                 hovertemplate = paste('%{text}'),
                 legendgroup = 'group2',
                 showlegend = ifelse(var == last.pos,TRUE,FALSE), 
                 line = list(color = "#7aa82a", 
                             width = 3, 
                             dash = "dot")
    ) %>%
    layout(xaxis = list(range = c(min(dep.pos$dat),
                                  max(dep.pos$dat)),
                        color = "white"),
           yaxis = list(color = "white", type = "log", tickmode = "linear"),
           annotations = list(text = ifelse(var=="LA_LIBERTAD","LA LIBERTAD",
                                            ifelse(var=="MADRE_DE_DIOS","MADRE DE DIOS",
                                                   ifelse(var=="SAN_MARTIN","SAN MARTIN",paste0("",var,"")))),
                              x = 0,y = 1.15,
                              yref = "paper",xref = "paper",
                              xanchor = "left",yanchor = "top",
                              showarrow = FALSE,
                              font = list(size = 16,
                                          color = "white")),
           paper_bgcolor="black",
           plot_bgcolor="black",
           legend = list(orientation = "h",  
                         xanchor = "center",
                         yanchor = "bottom",
                         x = 0.5,
                         y = -0.125,
                         font = list(color = "white")),
           showlegend =T)
})

subplot(plots,nrows=5, shareX = T, titleX = F) %>%
  layout(title = list(text = "Total de casos confirmados - Acumulado Logarítmico",
                      font = list(size = 24,
                                  color="white")),
         annotations = list(
           list(text = "Fecha de reporte",
                x = 0.5,
                y = -0.09,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color = "white")),
           list(text = "Total de casos confirmados",
                x = -0.05,
                y = 0.5,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color ="white"),
                textangle = -90)),
         hovermode = "closest",
         hoverdistance = 10,
         dragmode="pan",
         margin = list(l=75, r=0, b=65, t=60)
  ) %>%
  plotly_config



```


Casos Nuevos {.bg}
=====================================  

Mapas {.tabset data-width=250} 
-------------------------------------
### Casos nuevos

```{r, message=F, warning=F}
x <- c.dep %>% dplyr::mutate(pos.new = ifelse(pos.new==0,NA, pos.new)) %>% .$pos.new


labels.new <- sprintf(
  "%s
Casos: %s",
  c.dep$dep, c.dep$pos.new) %>% lapply(htmltools::HTML)

pal.cases <- colorNumeric( palette="RdPu", 
                           domain = log(x), na.color="transparent")

leaflet(c.dep) %>%
  map_tiles() %>%
  map_poly (y=x,
            z=labels.new) %>%
  addLegend("bottomleft", pal=pal.cases, values = log(x), title= 'Casos', labFormat = labelFormat(transform = function(x) round(exp(x))))%>%
  map_bounds()

rm(x)
```


Column 2 {.tabset data-width=300} 
-------------------------------------

### Diario y media móvil - Lineal

```{r, message=F, warning=F}
plot_ly(nac) %>%
  add_trace(x = ~dat, y = ~pos.new,
            type = 'scatter',
            mode = 'lines', name = 'Casos Nuevos por día',
            line = list(color = '#006b7d'), 
            text = paste(nac$days.end, "días desde hoy"),
            hovertemplate = paste('Fecha: %{x}',
                                  '
Nuevos Casos: %{y}
',
                                  '%{text}'))%>% 
  add_trace(x = ~dat, y = ~mav.pos.new, 
            type = 'scatter',
            mode = 'lines+markers', 
            name = 'Media Móvil de casos por día',
            line = list(color = '#ffa600'), 
            marker = list(color = '#ffa600'),
            text = paste(nac$days.end, "días desde hoy"),
            hovertemplate = ~paste('Fecha: %{x}',
                                   "
Media móvil: %{y:.0f}
",
                                   '%{text}'))  %>%
  add_segments(x = "2020-04-08", xend = "2020-04-08", 
               y = 0, yend=max(nac$pos.new),
               text="2020-04-08",name="Inicio de P.R's",
               hovertemplate = paste('%{text}'),
               legendgroup = 'group2',
               width=2, 
               line = list(color = "#7aa82a", 
                           width = 3, 
                           dash = "dot")
  )%>% 
  layout(title = ' Casos nuevos por día y media móvil',
         titlefont=list(color="white"),
         xaxis = list(title = "Fecha de reporte",
                      color="white"),
         yaxis = list(side = 'left', title = 'Casos nuevos por día', showgrid = FALSE, zeroline = FALSE,
                      color = "white"),
         yaxis2 = list(side = 'right', overlaying = "y",
                       title = 'Casos nuevos (lineal)', 
                       showgrid = FALSE, zeroline = FALSE,
                       color="#ffa600",
                       range = c(min(0),
                                 max(nac$pos.new))),
         legend = list(orientation = "h",  
                       xanchor = "center",
                       yanchor = "bottom",  
                       x = 0.5,
                       y = -0.15,
                       font = list(color = "white")),
         paper_bgcolor="black",
         plot_bgcolor="black",
         hovermode = "closest",
         hoverdistance = 50,
         dragmode="pan",
         margin = list(l=65, r=0, b=40, t=50)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines")
  )

```

### Media Móvil - logarítmica

```{r, message=F, warning=F}
plot_ly(nac) %>%
  add_trace(x = ~dat, y = ~mav.pos.new,
            type = 'scatter', mode="lines",name = 'Casos Nuevos',
            line = list(color = '#006b7d'), 
            text = paste(nac$days.end, "días desde hoy"),
            hovertemplate = paste('Fecha: %{x}',
                                  '
Nuevos Casos: %{y}
',
                                  '%{text}'))%>% 
  add_trace(x = ~dat, y = ~mav.pos.new, 
            type = 'scatter',
            mode = 'lines+markers', 
            name = 'Media Móvil',
            line = list(color = '#ffa600'), 
            marker = list(color = '#ffa600'),
            text = paste(nac$days.end, "días desde hoy"),
            hovertemplate = ~paste('Fecha: %{x}',
                                   "
Media móvil: %{y:.0f}
",
                                   '%{text}'))  %>%
  add_segments(x = "2020-04-08", xend = "2020-04-08", 
               y = 0, yend=max(nac$mav.pos.new),
               text="2020-04-08",name="Inicio de P.R's",
               hovertemplate = paste('%{text}'),
               legendgroup = 'group2',
               width=2, 
               line = list(color = "#7aa82a", 
                           width = 3, 
                           dash = "dot")
  )%>% 
  layout(title = 'Media móvil (7d) y casos nuevos por día - Perú',
         titlefont=list(color="white"),
         xaxis = list(title = "Fecha de reporte",
                      color="white"),
         yaxis = list(side = 'left', title = 'Casos nuevos por día', showgrid = FALSE, zeroline = FALSE,
                      color = "white", type ="log",tickmode="linear"),
         yaxis2 = list(side = 'right', overlaying = "y",
                       title = 'Media móvil de casos nuevos - 7 días (lineal)', 
                       showgrid = FALSE, zeroline = FALSE,
                       color="#ffa600",
                       range = c(min(0),
                                 max(nac$mav.pos.new))),
         legend = list(orientation = "h",  
                       xanchor = "center",
                       yanchor = "bottom",  
                       x = 0.5,
                       y = -0.15,
                       font = list(color = "white")),
         paper_bgcolor="black",
         plot_bgcolor="black",
         hovermode = "closest",
         hoverdistance = 50,
         dragmode="pan",
         margin = list(l=65, r=0, b=40, t=50)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines")
  )

```

### Duplicación de la media móvil

```{r, message=F, warning=F}
plot_ly(dup.nac)%>%
  add_trace(x = ~dat, y = ~pos, 
            type = 'scatter',
            mode = 'lines+markers', 
            name = 'Casos Acumulados',
            line = list(color = '#ffa600'), 
            marker = list(color = '#ffa600'),
            hovertemplate = ~paste("
Casos Acumulados: %{y:.d0}
"),
            legendgroup = 'group1') %>% 
  add_trace(x = ~dat, y = ~dup.1,
            mode = 'lines', 
            name = 'Casos se duplican en un (1) día',
            line = list(color = '#0e5871',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en un (1) día",
            hoverinfo = "text",
            legendgroup = 'group2') %>% 
  add_trace(x = ~dat, y = ~dup.2,
            mode = 'lines', 
            name = 'Casos se duplican en dos (2) días',
            line = list(color = '#006b7d',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en dos (2) días",
            hoverinfo = "text",
            legendgroup = 'group2') %>% 
  add_trace(x = ~dat, y = ~dup.3,
            mode = 'lines', 
            name = 'Casos se duplican en tres (3) días',
            line = list(color = '#007e7b',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en tres (3) días",
            hoverinfo = "text",
            legendgroup = 'group2') %>% 
  add_trace(x = ~dat, y = ~dup.4,
            mode = 'lines', 
            name = 'Casos se duplican en cuatro (4) días',
            line = list(color = '#008f6a',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en tres (4) días",
            hoverinfo = "text",
            legendgroup = 'group2')  %>% 
  layout(title = list(text= 'Tiempo de duplicación de casos acumulados',
                      font = list(
                        size = 20,
                        color="white")),
         xaxis = list(title = "",
                      range = c(as.Date(min(f.date)),max(date+15)),
                      color ="white",
                      tickformat= "%d - %b"),
         yaxis = list(side = 'left', 
                      title = list(text= 'Total de casos acumulados', 
                                   font = list(size = 16,
                                               color = "white")),   
                      type="log", automargin = T,
                      range = c(min(0),max(6)),
                      showgrid = FALSE, zeroline = FALSE,
                      tickmode = "linear",
                      tick0 = 0,
                      color ="white"),
         legend = list(orientation = "h",
                       yref = "paper",
                       xref = "paper",
                       xanchor = "right",
                       yanchor = "bottom",  
                       x = 1,
                       y = -0.25,
                       font = list(color = "white"), 
                       automargin = T),
         annotations = list(xref='paper',
                            yref='paper',
                            x=0,
                            y=-0.1,
                            xanchor='left',
                            yanchor='bottom',
                            text='Días desde el primer reporte',
                            showarrow=FALSE,
                            font = list(size = 16,
                                        color = "white")),
         paper_bgcolor="black",
         plot_bgcolor="black",
         hovermode = "closest",
         hoverdistance = 50,
         dragmode="pan",
         margin = list(l=0, r=0, b=100, t=65)
  ) %>%
  plotly_config( )

```


```{r}
dup.nac%>%
  dplyr::filter(days.end<=7 )%>%
  dplyr::mutate(days.start = as.numeric(difftime(dat,first(dat), units="days")),
                dummy = days.start+20,
                dup.1 = exp((log(2)/1)*days.start),
                dup.2 = exp((log(2)/2)*days.start),
                dup.3 = exp((log(2)/3)*days.start),
                dup.4 = exp((log(2)/4)*days.start),
                dup.6 = exp((log(2)/6)*days.start),
                dup.8 = exp((log(2)/8)*days.start),
                pos.sim = exp(((max(.$days.start)-min(.$days.start))/min(.$days.start))*(days.start))) %>%
  plot_ly()%>%
  add_trace(x = ~dat, y = ~pos.sim, 
            type = 'scatter',
            mode = 'lines+markers', 
            name = 'Casos Acumulados',
            line = list(color = '#ffa600'), 
            marker = list(color = '#ffa600'),
            hovertemplate = ~paste("
Casos Acumulados: %{y:.d0}
"),
            legendgroup = 'group1') %>% 
  add_trace(x = ~dat, y = ~dup.1,
            mode = 'lines', 
            name = 'Casos se duplican en un (1) día',
            line = list(color = '#0e5871',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en un (1) día",
            hoverinfo = "text",
            legendgroup = 'group2') %>% 
  add_trace(x = ~dat, y = ~dup.2,
            mode = 'lines', 
            name = 'Casos se duplican en dos (2) días',
            line = list(color = '#006b7d',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en dos (2) días",
            hoverinfo = "text",
            legendgroup = 'group2') %>% 
  add_trace(x = ~dat, y = ~dup.3,
            mode = 'lines', 
            name = 'Casos se duplican en tres (3) días',
            line = list(color = '#007e7b',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en tres (3) días",
            hoverinfo = "text",
            legendgroup = 'group2') %>% 
  add_trace(x = ~dat, y = ~dup.8,
            mode = 'lines', 
            name = 'Casos se duplican en ocho (8) días',
            line = list(color = '#008f6a',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en ocho (8) días",
            hoverinfo = "text",
            legendgroup = 'group2')  %>% 
  layout(title = '',
         titlefont=list(color="white"),
         xaxis = list(title = "Últimos 7 días",
                      range = c(as.Date(min(f.date)),max(date+15)),
                      color ="white"),
         yaxis = list(side = 'left', title = '', type="log",
                      range = c(min(0),max(3)),
                      showgrid = FALSE, zeroline = FALSE,
                      tickmode = "linear",
                      tick0 = 0,
                      color ="white"),
         legend = list(orientation = "h",  
                       xanchor = "center",
                       yanchor = "bottom",  
                       x = 0.5,
                       y = -0.25,
                       font = list(color = "white")),
         paper_bgcolor="black",
         plot_bgcolor="black",
         hovermode = "closest",
         hoverdistance = 50,
         dragmode="pan",
         margin = list(l=50, r=50, b=30, t=50)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines")
  )



```




















Column 3 {.tabset data-width=350} 
-------------------------------------
```{r, message=F, warning=F}
y<- dep.pos.imp.new 
colnames(y) <- paste(colnames(y), "2", sep = "_")

y<- y %>% 
  select(-c("dat_2","days.end_2")) %>% 
  cbind(dep.mav.pos.new)

```

### Lineal
```{r, message=F, warning=F}

plots <- lapply(vars.mav.new, function(var) {

  plot_ly(y) %>%
    add_lines(x = ~dat, 
              y = as.formula(paste0("~", var)),
              text = paste(y$days.end, "días desde hoy"),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Media Móvil: %{y:.2f}
',
                                    '%{text}'),
              name = ifelse(var == last.mav.new,"Media Móvil",var),
              legendgroup = 'group1',
              showlegend = ifelse(var == last.mav.new,TRUE,FALSE), 
              line = list(color = "#ffa600", 
                          width = 4)
    ) %>%
    add_segments(x = "2020-04-08", xend = "2020-04-08", 
                 y = 0, yend = max(y[paste0(var,"_2")],na.rm = T),
                 text="2020-04-08", name="Inicio de P.R's",
                 hovertemplate = paste('%{text}'),
                 legendgroup = 'group2',
                 showlegend = ifelse(var == last.mav.new,TRUE,FALSE), 
                 line = list(color = "#7aa82a", 
                             width = 3, 
                             dash = "dot")
    )%>%
    add_trace(x = ~dat, y = as.formula(paste0("~", var,"_2")),
              type = 'bar', name = 'Casos Nuevos',
              marker = list(color = '#006b7d'), 
              text = paste(y$days.end, "días desde hoy"),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Nuevos Casos: %{y}
',
                                    '%{text}'),
              showlegend = ifelse(var == last.mav.new,TRUE,FALSE)) %>%
    layout(xaxis = list(range = c(min(y$dat),
                                  max(y$dat)),
                        color = "white"),
           yaxis = list(color = "white"),
           annotations = list(text = ifelse(var=="LA_LIBERTAD","LA LIBERTAD",
                                            ifelse(var=="MADRE_DE_DIOS","MADRE DE DIOS",
                                                   ifelse(var=="SAN_MARTIN","SAN MARTIN",paste0("",var,"")))),
                              x = 0,y = 1.15,
                              yref = "paper",xref = "paper",
                              xanchor = "left",yanchor = "top",
                              showarrow = FALSE,
                              font = list(size = 16,
                                          color = "white")),
           paper_bgcolor="black",
           plot_bgcolor="black",
           legend = list(orientation = "h",  
                         xanchor = "center",
                         yanchor = "bottom",
                         x = 0.5,
                         y = -0.125,
                         font = list(color = "white")),
           showlegend =T)
})

subplot(plots,nrows=5, shareX = T, titleX = F) %>%
  layout(title = list(text = "Media móvil (7 días) de casos nuevos",
                      font = list(size = 24,
                                  color="white")),
         annotations = list(
           list(text = "Fecha de reporte",
                x = 0.5,
                y = -0.09,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color = "white")),
           list(text = "Media móvil - Número de casos",
                x = -0.05,
                y = 0.5,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color ="white"),
                textangle = -90)),
         hovermode = "closest",
         hoverdistance = 10,
         dragmode="pan",
         margin = list(l=75, r=0, b=65, t=60)
  ) %>%
  plotly_config()

```

### Logaritmica 
```{r, message=F, warning=F}

plots <- lapply(vars.mav.new, function(var) {
  
  plot_ly(y) %>%
    add_lines(x = ~dat, 
              y = as.formula(paste0("~", var)),
              text = paste(y$days.end, "días desde hoy"),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Media Móvil: %{y:.2f}
',
                                    '%{text}'),
              name = ifelse(var == last.mav.new,"Media Móvil",var),
              legendgroup = 'group1',
              showlegend = ifelse(var == last.mav.new,TRUE,FALSE), 
              line = list(color = "#ffa600", 
                          width = 4)
    ) %>%
    add_segments(x = "2020-04-08", xend = "2020-04-08", 
                 y = 0, yend = max(y[paste0(var,"_2")],na.rm = T),
                 text="2020-04-08", name="Inicio de P.R's",
                 hovertemplate = paste('%{text}'),
                 legendgroup = 'group2',
                 showlegend = ifelse(var == last.mav.new,TRUE,FALSE), 
                 line = list(color = "#7aa82a", 
                             width = 3, 
                             dash = "dot")
    )%>%
    add_trace(x = ~dat, y = as.formula(paste0("~", var,"_2")),
              type = 'bar', name = 'Casos Nuevos',
              marker = list(color = '#006b7d'), 
              text = paste(y$days.end, "días desde hoy"),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Nuevos Casos: %{y}
',
                                    '%{text}'),
              showlegend = ifelse(var == last.mav.new,TRUE,FALSE)) %>%
    layout(xaxis = list(range = c(min(y$dat),
                                  max(y$dat)),
                        color = "white"),
           yaxis = list(color = "white", type="log"),
           annotations = list(text = ifelse(var=="LA_LIBERTAD","LA LIBERTAD",
                                            ifelse(var=="MADRE_DE_DIOS","MADRE DE DIOS",
                                                   ifelse(var=="SAN_MARTIN","SAN MARTIN",paste0("",var,"")))),
                              x = 0,y = 1.15,
                              yref = "paper",xref = "paper",
                              xanchor = "left",yanchor = "top",
                              showarrow = FALSE,
                              font = list(size = 16,
                                          color = "white")),
           paper_bgcolor="black",
           plot_bgcolor="black",
           legend = list(orientation = "h",  
                         xanchor = "center",
                         yanchor = "bottom",
                         x = 0.5,
                         y = -0.125,
                         font = list(color = "white")),
           showlegend =T)
})

subplot(plots,nrows=5, shareX = T, titleX = F) %>%
  layout(title = list(text = "Media móvil (7 días) de casos nuevos",
                      font = list(size = 24,
                                  color="white")),
         annotations = list(
           list(text = "Fecha de reporte",
                x = 0.5,
                y = -0.09,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color = "white")),
           list(text = "Media móvil - Número de casos",
                x = -0.05,
                y = 0.5,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color ="white"),
                textangle = -90)),
         hovermode = "closest",
         hoverdistance = 10,
         dragmode="pan",
         margin = list(l=75, r=0, b=65, t=60)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines")
  )

```


Fallecidos {.bg}
===================================== 

Column 1 {.tabset data-width=250} 
-------------------------------------



Column 1 {.tabset data-width=300} 
-------------------------------------



Column 1 {.tabset data-width=350} 
-------------------------------------

Fallecidos Nuevos {.bg}
===================================== 


Diagnósticos {.bg}
===================================== 



Diagnósticos Nuevos {.bg}
=====================================